ID A0A161SJG6_9BACT Unreviewed; 644 AA.
AC A0A161SJG6; A0A161SJ42;
DT 06-JUL-2016, integrated into UniProtKB/TrEMBL.
DT 06-JUL-2016, sequence version 1.
DT 27-MAR-2024, entry version 35.
DE RecName: Full=DNA gyrase subunit B {ECO:0000256|HAMAP-Rule:MF_01898};
DE EC=5.6.2.2 {ECO:0000256|HAMAP-Rule:MF_01898};
GN Name=gyrB {ECO:0000256|HAMAP-Rule:MF_01898,
GN ECO:0000313|EMBL:KZD19782.1};
GN ORFNames=AO394_01625 {ECO:0000313|EMBL:KZD19782.1}, GX473_05010
GN {ECO:0000313|EMBL:NLI02672.1};
OS Candidatus Fermentibacter daniensis.
OC Bacteria; Candidatus Fermentibacteria; Candidatus Fermentibacteria (class);
OC Candidatus Fermentibacterales; Candidatus Fermentibacteraceae;
OC Fermentibacter.
OX NCBI_TaxID=1729713 {ECO:0000313|EMBL:KZD19782.1, ECO:0000313|Proteomes:UP000076793};
RN [1] {ECO:0000313|EMBL:KZD19782.1, ECO:0000313|Proteomes:UP000076793}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=Dam_1 {ECO:0000313|EMBL:KZD19782.1};
RX PubMed=27058503;
RA Kirkegaard R.H., Dueholm M.S., McIlroy S.J., Nierychlo M., Karst S.M.,
RA Albertsen M., Nielsen P.H.;
RT "Genomic insights into members of the candidate phylum Hyd24-12 common in
RT mesophilic anaerobic digesters.";
RL ISME J. 0:0-0(2016).
RN [2] {ECO:0000313|EMBL:NLI02672.1, ECO:0000313|Proteomes:UP000567630}
RP NUCLEOTIDE SEQUENCE [LARGE SCALE GENOMIC DNA].
RC STRAIN=AS4DglBPLU_32 {ECO:0000313|EMBL:NLI02672.1};
RX PubMed=32123542;
RA Campanaro S., Treu L., Rodriguez-R L.M., Kovalovszki A., Ziels R.M.,
RA Maus I., Zhu X., Kougias P.G., Basile A., Luo G., Schluter A.,
RA Konstantinidis K.T., Angelidaki I.;
RT "New insights from the biogas microbiome by comprehensive genome-resolved
RT metagenomics of nearly 1600 species originating from multiple anaerobic
RT digesters.";
RL Biotechnol. Biofuels 13:25-20(2020).
CC -!- FUNCTION: A type II topoisomerase that negatively supercoils closed
CC circular double-stranded (ds) DNA in an ATP-dependent manner to
CC modulate DNA topology and maintain chromosomes in an underwound state.
CC Negative supercoiling favors strand separation, and DNA replication,
CC transcription, recombination and repair, all of which involve strand
CC separation. Also able to catalyze the interconversion of other
CC topological isomers of dsDNA rings, including catenanes and knotted
CC rings. Type II topoisomerases break and join 2 DNA strands
CC simultaneously in an ATP-dependent manner. {ECO:0000256|HAMAP-
CC Rule:MF_01898}.
CC -!- CATALYTIC ACTIVITY:
CC Reaction=ATP-dependent breakage, passage and rejoining of double-
CC stranded DNA.; EC=5.6.2.2; Evidence={ECO:0000256|ARBA:ARBA00000185,
CC ECO:0000256|HAMAP-Rule:MF_01898};
CC -!- COFACTOR:
CC Name=Mg(2+); Xref=ChEBI:CHEBI:18420;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC Name=Mn(2+); Xref=ChEBI:CHEBI:29035;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC Name=Ca(2+); Xref=ChEBI:CHEBI:29108;
CC Evidence={ECO:0000256|HAMAP-Rule:MF_01898};
CC Note=Binds two Mg(2+) per subunit. The magnesium ions form salt bridges
CC with both the protein and the DNA. Can also accept other divalent metal
CC cations, such as Mn(2+) or Ca(2+). {ECO:0000256|HAMAP-Rule:MF_01898};
CC -!- SUBUNIT: Heterotetramer, composed of two GyrA and two GyrB chains. In
CC the heterotetramer, GyrA contains the active site tyrosine that forms a
CC transient covalent intermediate with DNA, while GyrB binds cofactors
CC and catalyzes ATP hydrolysis. {ECO:0000256|HAMAP-Rule:MF_01898}.
CC -!- SUBCELLULAR LOCATION: Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01898}.
CC -!- MISCELLANEOUS: Few gyrases are as efficient as E.coli at forming
CC negative supercoils. Not all organisms have 2 type II topoisomerases;
CC in organisms with a single type II topoisomerase this enzyme also has
CC to decatenate newly replicated chromosomes. {ECO:0000256|HAMAP-
CC Rule:MF_01898}.
CC -!- SIMILARITY: Belongs to the type II topoisomerase GyrB family.
CC {ECO:0000256|ARBA:ARBA00010708, ECO:0000256|HAMAP-Rule:MF_01898}.
CC -!- CAUTION: The sequence shown here is derived from an EMBL/GenBank/DDBJ
CC whole genome shotgun (WGS) entry which is preliminary data.
CC {ECO:0000313|EMBL:KZD19782.1}.
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DR EMBL; LKHB01000057; KZD19782.1; -; Genomic_DNA.
DR EMBL; JAAYWI010000037; NLI02672.1; -; Genomic_DNA.
DR AlphaFoldDB; A0A161SJG6; -.
DR STRING; 1729713.AO395_02800; -.
DR Proteomes; UP000076793; Unassembled WGS sequence.
DR Proteomes; UP000567630; Unassembled WGS sequence.
DR GO; GO:0005694; C:chromosome; IEA:InterPro.
DR GO; GO:0005737; C:cytoplasm; IEA:UniProtKB-SubCell.
DR GO; GO:0005524; F:ATP binding; IEA:UniProtKB-UniRule.
DR GO; GO:0003677; F:DNA binding; IEA:UniProtKB-KW.
DR GO; GO:0003918; F:DNA topoisomerase type II (double strand cut, ATP-hydrolyzing) activity; IEA:UniProtKB-UniRule.
DR GO; GO:0046872; F:metal ion binding; IEA:UniProtKB-KW.
DR GO; GO:0006265; P:DNA topological change; IEA:UniProtKB-UniRule.
DR GO; GO:0006261; P:DNA-templated DNA replication; IEA:UniProtKB-UniRule.
DR CDD; cd16928; HATPase_GyrB-like; 1.
DR CDD; cd00822; TopoII_Trans_DNA_gyrase; 1.
DR CDD; cd03366; TOPRIM_TopoIIA_GyrB; 1.
DR Gene3D; 3.30.230.10; -; 1.
DR Gene3D; 3.40.50.670; -; 1.
DR Gene3D; 3.30.565.10; Histidine kinase-like ATPase, C-terminal domain; 1.
DR HAMAP; MF_01898; GyrB; 1.
DR InterPro; IPR002288; DNA_gyrase_B_C.
DR InterPro; IPR011557; GyrB.
DR InterPro; IPR003594; HATPase_C.
DR InterPro; IPR036890; HATPase_C_sf.
DR InterPro; IPR020568; Ribosomal_Su5_D2-typ_SF.
DR InterPro; IPR014721; Ribsml_uS5_D2-typ_fold_subgr.
DR InterPro; IPR001241; Topo_IIA.
DR InterPro; IPR013760; Topo_IIA-like_dom_sf.
DR InterPro; IPR000565; Topo_IIA_B.
DR InterPro; IPR013759; Topo_IIA_B_C.
DR InterPro; IPR013506; Topo_IIA_bsu_dom2.
DR InterPro; IPR018522; TopoIIA_CS.
DR InterPro; IPR006171; TOPRIM_domain.
DR InterPro; IPR034160; TOPRIM_GyrB.
DR NCBIfam; TIGR01059; gyrB; 1.
DR PANTHER; PTHR45866:SF1; DNA GYRASE SUBUNIT B, MITOCHONDRIAL; 1.
DR PANTHER; PTHR45866; DNA GYRASE/TOPOISOMERASE SUBUNIT B; 1.
DR Pfam; PF00204; DNA_gyraseB; 1.
DR Pfam; PF00986; DNA_gyraseB_C; 1.
DR Pfam; PF02518; HATPase_c; 1.
DR Pfam; PF01751; Toprim; 1.
DR PRINTS; PR01159; DNAGYRASEB.
DR PRINTS; PR00418; TPI2FAMILY.
DR SMART; SM00387; HATPase_c; 1.
DR SMART; SM00433; TOP2c; 1.
DR SUPFAM; SSF55874; ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase; 1.
DR SUPFAM; SSF54211; Ribosomal protein S5 domain 2-like; 1.
DR SUPFAM; SSF56719; Type II DNA topoisomerase; 1.
DR PROSITE; PS00177; TOPOISOMERASE_II; 1.
DR PROSITE; PS50880; TOPRIM; 1.
PE 3: Inferred from homology;
KW ATP-binding {ECO:0000256|ARBA:ARBA00022840, ECO:0000256|HAMAP-
KW Rule:MF_01898}; Cytoplasm {ECO:0000256|HAMAP-Rule:MF_01898};
KW DNA-binding {ECO:0000256|ARBA:ARBA00023125};
KW Isomerase {ECO:0000256|ARBA:ARBA00023235, ECO:0000256|HAMAP-Rule:MF_01898};
KW Magnesium {ECO:0000256|ARBA:ARBA00022842, ECO:0000256|HAMAP-Rule:MF_01898};
KW Metal-binding {ECO:0000256|ARBA:ARBA00022723, ECO:0000256|HAMAP-
KW Rule:MF_01898};
KW Nucleotide-binding {ECO:0000256|ARBA:ARBA00022741, ECO:0000256|HAMAP-
KW Rule:MF_01898};
KW Topoisomerase {ECO:0000256|ARBA:ARBA00023029, ECO:0000256|HAMAP-
KW Rule:MF_01898}.
FT DOMAIN 428..543
FT /note="Toprim"
FT /evidence="ECO:0000259|PROSITE:PS50880"
FT BINDING 434
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 508
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="1"
FT /ligand_note="catalytic"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 508
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT BINDING 510
FT /ligand="Mg(2+)"
FT /ligand_id="ChEBI:CHEBI:18420"
FT /ligand_label="2"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 459
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
FT SITE 462
FT /note="Interaction with DNA"
FT /evidence="ECO:0000256|HAMAP-Rule:MF_01898"
SQ SEQUENCE 644 AA; 71034 MW; B3AD80D35187863F CRC64;
MSQLKGERYD AGSIQVLEGL EAVRKRPSMY IGSTSQAGLH HLVWEVVDNS VDEAQAGFCD
RIDVRLLDGD VVSVRDNGRG IPIDPHPKFN RPALEIVLTK LHAGGKFDSN AYKVSGGLHG
VGLSVVNALS EWLVVEVSKN GRLYSQRFER GIPVSELSVC GDSSETGTLV TFRPDSEIFE
ETSFGFDTLS RRLRELAFLN RGLSIGLRDE RQDGTGRSHD FMYEGGIVSL VQFLNESRHT
LHADPIYISK DSELEDGSTM LVECAIQYDS GYQEEIFSFA NNINTIDGGS HLTGFRAALT
RGLNDYATAF GLFKKSDESF SGNDVKEGLT AVISVKLSHP QFEGQTKTRL GNRDVKGAVE
SIIYSGLSTF LEENPAVARK LIQKCQETSA ARLAARNARE LTRRKSALET ASLPGKLADC
TSTDPVESEI FIVEGDSAGG SAKQGRNRFN QAILPLRGKI LNVEKAPLHK ILGNAEIKAM
VTAIGTGIGE EDFDPARLRY GRIIIMTDAD VDGAHIRTLL LTFFYRYMPA LIEQGNIFIA
QPPLFGIHAG KKSIYAYSEK ERDRILEEIG TDKATVQRYK GLGEMNPSQL WATAMDPSTR
TILKIRMEDA VEASRIFSVL MGDEVLPRRE FIQEHASEVR NLDV
//
